Cohesin loss eliminates all loop domains, leading to links among superenhancers and downregulation of nearby genes

Abstract

SUMMARY:The human genome folds to create thousands of intervals, called "contact domains," that exhibit enhanced contact frequency within themselves. "Loop domains" form because of tethering between two loci -almost always bound by CTCF and cohesin -lying on the same chromosome. "Compartment domains" form when genomic intervals with similar histone marks co-segregate. Here, we explore the effects of degrading cohesin. All loop domains are eliminated, but neither compartment domains nor histone marks are affected. Loci in different compartments that had been in the same loop domain become more segregated. Loss of loop domains does not lead to widespread ectopic gene activation, but does affect a significant minority of active genes. In particular, cohesin loss causes superenhancers to co-localize, forming hundreds of links within and across chromosomes, and affecting the regulation of nearby genes. Cohesin restoration quickly reverses these effects, consistent with a model where loop extrusion is rapid. INTRODUCTION:Many studies have shown that the insulator protein CTCF and the ring-shaped cohesin complex colocalize on chromatin (Parelho et al., 2008; Rubio et al., 2008; Wendt et al., 2008) and lie at the anchors of loops (Heidari et al., 2014; Rao et al., 2014; Splinter et al., 2006; Tang et al., 2015) and the boundaries of contact domains (sometimes called "topologically constrained domains", "topologically . CC-BY-NC-ND 4.0 International license peer-reviewed) is the author/funder. It is made available under aThe copyright holder for this preprint (which was not . http://dx.doi.org/10.1101/139782 doi: bioRxiv preprint first posted online May. 18, 2017; 2 associated domains", or "physical domains") (Dixon et al., 2012; Lieberman-Aiden et al., 2009; Nora et al., 2012; Phillips-Cremins et al., 2013; Rao et al., 2014; Sexton et al., 2012). These findings suggest that these proteins play a role in regulating genome folding (Benabdallah and Bickmore, 2015; Dekker and Misteli, 2015; Lupiáñez et al., 2016; Merkenschlager and Nora, 2016; Phillips-Cremins and Corces, 2013; Uhlmann, 2016). Similarly, deletion of individual CTCF sites can interfere with loop and contact domain formation (Guo et al., 2015; Narendra et al., 2015;Sanborn et al., 2015; de Wit et al., 2015). However, low-resolution experiments examining genome-wide depletion of CTCF and cohesin have thus far observed only limited effects on chromosome architecture, reporting that compartments and contact domains still appear to be present (Seitan et al., 2013; Sofueva et al., 2013; Zuin et al., 2014). These results have made it difficult to ascertain the role of CTCF and cohesin in the regulation of genome topology at the chromosome scale.Here, we examine the effects of cohesin loss on nuclear architecture, epigenetic state, and transcription. By generating maps of DNA-DNA contacts of much higher resolution, we are able to characterize the effects of global cohesin loss on nuclear architecture more clearly than in earlier studies. We demonstrate that ...

Two independent modes of chromatin organization revealed by cohesin removal

“…Emergence of fine compartmentalization, however, was not reported likely due to the limited number of nuclei. Two other preprints reporting degron-mediated depletion of Rad21/Scc1 in human cell lines observed concordant effects on TADs, peaks, and compartmentalization to our study 36,37 . Rao et al also identified intriguing emergent “loop” cliques enriched in super-enhancers upon cohesin depletion 37 .…”

“…Two other preprints reporting degron-mediated depletion of Rad21/Scc1 in human cell lines observed concordant effects on TADs, peaks, and compartmentalization to our study 36,37 . Rao et al also identified intriguing emergent “loop” cliques enriched in super-enhancers upon cohesin depletion 37 . We also observed such features in our primary hepatocytes using a new Hi-C browser 38 , though we note that in both cases these patterns do not resemble the sharp cis -only focal patterns of CTCF-associated Hi-C peaks commonly referred to as loops 12 .…”

Genome‐Wide Maps of Transcription Regulatory Elements and Transcription Enhancers in Development and Disease

“…Additionally, the cohesin complex has been found to associate with CTCF to aid in cohesin binding at enhancers (80). Interestingly, depletion of cohesin results in the elimination of chromatin loops, however there is little transcriptional effect (85). One debate that remains in the field is whether cohesin depletion eliminates TAD architecture (85, 92), or is solely limited to inter-TAD loops (93, 96, 124).…”

“…Interestingly, depletion of cohesin results in the elimination of chromatin loops, however there is little transcriptional effect (85). One debate that remains in the field is whether cohesin depletion eliminates TAD architecture (85, 92), or is solely limited to inter-TAD loops (93, 96, 124). Disruption of cohesin causes a downregulation of super-enhancer-regulated genes (48).…”

Coolpup.py:versatile pile-up analysis of Hi-C data

“…Since its inception in the current form (Rao et al, 2014), originally termed APA ("Aggregate Peak Analysis"), pile-up analysis has been used in numerous publications, both to analyse single-cell Hi-C data (Flyamer et al, 2017;Gassler et al, 2017;Nagano et al, 2017) and as a general way of quantifying feature strength (Fudenberg et al, 2016;Schwarzer et al, 2017;Bonev et al, 2017;Nora et al, 2017;McLaughlin et al, 2019;Rao et al, 2017;Díaz et al, 2018;Kruse et al, 2019;Abdennur et al, 2018;Rowley et al, 2019;Krietenstein et al, 2019;Hsieh et al, 2019). A visual interactive tool to semi-manually classify and pile-up predefined regions has also been developed (Lekschas et al, 2018).…”